Deciphering fundamental biological processes involving protein-nucleic acid interactions at the molecular level

摘要 舒马赫实验室的中心重点是推断支配基本原理的分子原理。 涉及蛋白质-核酸相互作用的生物过程。我们最近的工作在转录方面取得了进展 微生物中的网络和DNA分离。后一项研究揭示了对分子的关键洞察 使用肌动蛋白和微管蛋白类NTPase分离细菌的简化系统所利用的机制 质粒。然而，控制最常见的细菌分离系统的分子机制(S)， 基于Walker-box的系统仍然不清楚，并且代表了我们研究的一个主要焦点。引人注目的是，我们的 最近对第一个古生菌分离系统的研究表明，它利用了一种类似细菌的 Walker-box NTPase驱动DNA分离，表明Walker-box分离机器可能是 生物学中最普遍的DNA分离模块类型。这些调查还显示， 古细菌分离PARB蛋白含有一个类似于CenpA的折叠，CenpA是介导DNA的组蛋白同源物 真核生物中的分离。因此，这些研究揭示了种族隔离中可能的进化联系 生活的三个领域之间的机械。我们最新的工作提供了第一个分子观点 与DNA和PARB结合的Walker-box NTPase。这些数据结合了细胞和生化研究 使我们能够为Walker-box分离提出一个通用的、基于非聚合物的模型，我们将对其进行测试 使用细胞和分子方法。我们在枯草杆菌氮素调节回路方面的工作有 揭示了一种新的DNA结合方式和一种新的调节机制，涉及 氮平衡，谷氨酰胺合成酶。实验室的一个新方向是推断分子 链霉菌生长的控制机制与其产生抗生素的过程相吻合 (次生代谢物)。事实上，链霉菌产生了我们目前使用的大部分抗生素以及过多的 生物医学上重要的化合物。在接下来的5年里，我们将扩大这些努力，但也会增加蜂窝、 遗传学和低温电子显微镜方法，以提供这些系统的更完整的图景。这些 值得注意的是，调查与实验室对微生物多重耐药和多重药物的兴趣相交 宽容。事实上，虽然这些研究的总体目标是确定基本的生物学原理 这些正在进行的研究还将为抗菌疗法的发展提供新的目标， 鉴于耐多药微生物的惊人增长和新药物的稀缺，迫切需要 抗菌药正在研发中。

ABSTRACT The central focus of the Schumacher laboratory is to deduce molecular principles that govern fundamental biological processes involving protein-nucleic acid interactions. Our recent work has honed in on transcription networks and DNA segregation in microbes. The latter studies have uncovered key insights into the molecular mechanisms utilized by simplified systems employing actin-like and tubulin-like NTPases to segregate bacterial plasmids. However, the molecular mechanism(s) controlling the most common bacterial segregation systems, the Walker-box based systems, remain unclear and represent a major focus of our research. Strikingly, our recent studies characterizing the first archaeal segregation system revealed that it utilizes a bacterial-like Walker-box NTPase to drive DNA segregation, indicating that Walker-box segregation machineries may be the most ubiquitous type of DNA segregation modules in biology. These investigations also revealed that the archaeal segregation ParB protein harbors a fold similar to CenpA, the histone homolog that mediates DNA segregation in eukaryotes. Thus, these studies uncovered possible evolutionary linkages in segregation machineries between the 3 domains of life. Our most recent work has provided the first molecular views of Walker-box NTPases bound to DNA and ParB. These data combined with cellular and biochemical studies have allowed us to propose a general, non-polymer based model for Walker-box segregation that we will test using cellular and molecular approaches. Our work on the nitrogen regulatory circuitry in B. subtilis has revealed new DNA binding modalities and a novel regulatory mechanism involving the direct enzyme of nitrogen homeostasis, glutamine synthetase. A new direction for the lab is to deduce the molecular mechanisms controlling Streptomyces development, which coincides with their production of antibiotics (secondary metabolites). Indeed, Streptomyces generate most of our current antibiotics as well as a plethora of biomedically important compounds. In the next 5 years we will expand on these efforts, but also add cellular, genetic and cryo-EM microscopy approaches to provide a more complete picture of these systems. These investigations notably intersect with the lab's interests in microbial multidrug resistance and multidrug tolerance. Indeed, while the overall goals of these studies are to determine fundamental biological principles these ongoing studies will also provide novel targets for the development of antimicrobial therapeutics, which are urgently needed given the alarming rise of multidrug resistant microbes and the scarcity of new antimicrobials in the pipeline.